title: Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter.
abstract: Genome-wide association studies have the potential to identify causal genetic factors underlying important phenotypes but have rarely been performed in bacteria. We present an association mapping method that takes into account the clonal population structure of bacteria and is applicable to both core and accessory genome variation. Campylobacter is a common cause of human gastroenteritis as a consequence of its proliferation in multiple farm animal species and its transmission via contaminated meat and poultry. We applied our association mapping method to identify the factors responsible for adaptation to cattle and chickens among 192 Campylobacter isolates from these and other host sources. Phylogenetic analysis implied frequent host switching but also showed that some lineages were strongly associated with particular hosts. A seven-gene region with a host association signal was found. Genes in this region were almost universally present in cattle but were frequently absent in isolates from chickens and wild birds. Three of the seven genes encoded vitamin B5 biosynthesis. We found that isolates from cattle were better able to grow in vitamin B5-depleted media and propose that this difference may be an adaptation to host diet.
authors.affiliation: Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom.
authors.forename: Samuel K
authors.initials: SK
authors.lastname: Sheppard
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.forename: Guillaume
authors.initials: G
authors.lastname: Meric
authors.forename: Alicia
authors.initials: A
authors.lastname: Torralbo
authors.forename: Keith A
authors.initials: KA
authors.lastname: Jolley
authors.forename: David J
authors.initials: DJ
authors.lastname: Kelly
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.forename: Martin C J
authors.initials: MC
authors.lastname: Maiden
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Daniel
authors.initials: D
authors.lastname: Falush
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D053898:Biosynthetic Pathways / Q000235:genetics*; D002167:Campylobacter / Q000235:genetics*; D002417:Cattle / Q000382:microbiology*; D002645:Chickens / Q000382:microbiology; D016000:Cluster Analysis; D019295:Computational Biology; D005828:Genetics, Population; D016680:Genome, Bacterial / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods*; D058507:Host Specificity / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010205:Pantothenic Acid / Q000096:biosynthesis*; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D010205:Pantothenic Acid
keywords: evolution; genomics; host adaptation; transmission ecology